rs17066879

Variant names:

• chr18-60397626-A-T
• rs17066879
• ENST00000650201.1:n.113+68281A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650201.1(ENSG00000285681):​n.113+68281A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,076 control chromosomes in the GnomAD database, including 2,510 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.18 (2510 hom., cov: 32)
• Consequence: ENSG00000285681 ENST00000650201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226
• Publications: 4 publications found

Genes affected

ENSG00000285681 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285681	ENST00000650201.1	n.113+68281A>T		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1	n.156+68281A>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27122 AN: 151958 Hom.: 2500 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0372

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.135

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.159

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.179 AC: 27157 AN: 152076 Hom.: 2510 Cov.: 32 AF XY: 0.174 AC XY: 12900 AN XY: 74336

African (AFR) AF: 0.196 AC: 8139 AN: 41490

American (AMR) AF: 0.140 AC: 2135 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 460 AN: 3472

East Asian (EAS) AF: 0.0375 AC: 194 AN: 5172

South Asian (SAS) AF: 0.162 AC: 783 AN: 4824

European-Finnish (FIN) AF: 0.160 AC: 1693 AN: 10594

Middle Eastern (MID) AF: 0.141 AC: 41 AN: 290

European-Non Finnish (NFE) AF: 0.194 AC: 13151 AN: 67956

Other (OTH) AF: 0.157 AC: 331 AN: 2106

Alfa AF: 0.185 Hom.: 350

Bravo AF: 0.178

Asia WGS AF: 0.0940 AC: 325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.24
DANN	Benign	0.38
PhyloP100		-0.23

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17066879; hg19: chr18-58064859;